Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate Ga0059261_0767 Ga0059261_0767 glucose/galactose transporter
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Korea:Ga0059261_0767 Length = 434 Score = 336 bits (862), Expect = 7e-97 Identities = 194/431 (45%), Positives = 268/431 (62%), Gaps = 27/431 (6%) Query: 4 VSSTTPQNGSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLV 63 +SST P +G A + +F + +LFFI+G IT+LND++IP LK +F L+YTQAMLV Sbjct: 8 LSSTDPASGDAQGINAPDLQVF--VFALFFIFGGITSLNDVIIPKLKELFTLNYTQAMLV 65 Query: 64 QFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFV 123 QFCFF AY ++ L+ ++GY+RG + GL TM GCLLF PAS Y +FL ALFV Sbjct: 66 QFCFFTAYLVIGIPGAKLVKKLGYMRGAVAGLLTMMVGCLLFIPASQYATYGVFLFALFV 125 Query: 124 LASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAA---- 179 LASG+ I+QV ANP ++ LG TA SRL AQA NSLG T+ P+ GS+LI G+ A Sbjct: 126 LASGVVIVQVVANPLISLLGKPETAHSRLTFAQAFNSLGTTVFPIVGSILILGSLATVTA 185 Query: 180 -------------GTHEAVQLPYLLLAAVIGIIA-VGFIF---LGGKVKHADMGVDHRHK 222 +A+ YL +AA + ++A V ++F L G+ A G+ Sbjct: 186 DQLSGPALEAYRVAESKAIMHGYLGIAAALAVVAGVVWLFRNRLKGERHQASAGLAGL-- 243 Query: 223 GSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMI 282 LL R GAL IFLYVGAEVSIGS +VNY +P + GL E++A +L+ +YWGGAM+ Sbjct: 244 -DLLGRPRFGFGALCIFLYVGAEVSIGSLIVNYLMQPGVMGLQEQAAGKLIGFYWGGAMV 302 Query: 283 GRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFT 342 GRF G+ L R +P +LA AV A L++++ ++G +A ++LA+G NSIMFPTIF+ Sbjct: 303 GRFIGSGLMRVISPGKLLAFVAVGAVALILISTNTTGHVAGYSLLAIGLMNSIMFPTIFS 362 Query: 343 LAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVG-VQLSFIVPTFCYFYICWYAF 401 LA E LG + GSG++ AI GGA++P+ G +AD G + L+ I+P CY I + + Sbjct: 363 LASEKLGGRAADGSGIINIAIFGGAVVPLATGALADATGSLGLALILPAICYAIIAGFGY 422 Query: 402 FARNRMNGETA 412 +AR G A Sbjct: 423 YARRPYAGPVA 433 Lambda K H 0.329 0.142 0.425 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 510 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 413 Length of database: 434 Length adjustment: 32 Effective length of query: 381 Effective length of database: 402 Effective search space: 153162 Effective search space used: 153162 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory